Of Fireflies
by Shazza72
Summary: Is John Sheppard losing his mind? Taunted by his own odd behavior he begins to wonder. And who or what is behind the strange dreams he keeps having?
1. Chapter 1

Katie woke slowly, not wanting to open her eyes, hoping to drift off to sleep again. She was so comfy and warm, and damn he smelt so good! Her lethargic body was about to drift off to sleep again when her brain suddenly re-engaged.

He! There was a man in her bed! In a panic she quickly jerked backwards, only to let out a yelp as she fell off the edge of the bed tangled in the sheet.

"What the hell?" The man sat up in alarm. He spluttered, looking around and finally noticing Katie on the floor. "What are you doing in here?" He demanded to know.

"Keep away from me!" She shouted at him, pulling the sheet around her protectively.

The man went to stand up and froze.

"Where are my clothes?" He asked, and Katie wasn't sure if he was talking to himself or to her.

She scooted back towards the wall, reaching out a hand to try find her bedside table where she had left her radio. On the other side of the bed there was the sound of rummaging and suddenly the bed side light clicked on.

Blinking in the sudden brightness Katie recognised the man as he turned to face her. Lt Colonel John Sheppard.

"What are you doing in here?" He asked again, hastily yanking on his pants.

"My room." Katie managed to say. She had never met him, but everyone knew who John Sheppard was.

"What?" He asked, and looking around confused, silhouetted in the lamp light. Then with shocked look on his face. "Did we...?" She could see his Adams apple bobbing as he swallowed.

"No I, I... no!" She stammered. "I locked the door..." She started.

"Do I know you?" He frowned.

Katie shook her head.

"Then how...?" He scrubbed a hand over his face and through his already messy hair. "I don't remember coming here." He admitted. He looked as confused as she felt.

"You weren't here last night." She told him, meaning that she was alone when she went to bed and fell asleep.

"Right!" He drawled. "I'd better go!" He leant down and swiped something from the floor.

"Yeah." She told him.

Sheppard stood up and pulled his t-shirt over his head. He jammed his feet into his boots and headed for the door.

"Sorry." He muttered as the door closed behind him.

Out in the hallway, the security camera picked up a very dishevelled looking Colonel, looking left and right to orient himself before he strode off down the hall, boots flapping.

Back in his own room, John wondered what the hell had just happened? He had woken up in bed with a woman he did not know, having no idea how he got there and why he'd been naked? Sure it wasn't the first time he'd woken up in bed with a woman, but usually he had some recollection of actually meeting her first. Looking at his watch, it was nearly 6am, so he decided to head straight for the shower.

Two levels down, Katie was also in the shower. Her heart rate had slowed down, but the confusion wasn't going away. How did Colonel Sheppard end up in her bed? She knew that nothing had happened, sexually at least, but what was he doing there? How did he get into her room? Did this sort of thing happen often on Atlantis she wondered?

Katie had only been in the city for just under 3 weeks and had seen the Colonel come into the infirmary for his post-mission checkups with the Doctors, but they had never spoken or even met. Katie was pretty sure she would have remembered, Sheppard was kind of hard to forgot. He was probably the hottest guy on the base, and a big favourite amongst the nurses in the infirmary.

Maybe she should look up that psychologist and ask about this stuff? As she made the bed, she could still smell Sheppard on the pillow, so she stripped off the bedclothes. She dressed and collected up her dirty clothes. Might as well do her laundry before going to work. At least she could wash the evidence of her visitor off her sheets.

Katie didn't end up talking to the psychologist but she did talk to some of the other nurses about strange things happening on Atlantis. Apparently strange stuff happened all the time. She shrugged when they asked for specifics but she refused to elaborate. It was just too weird, and everyone seemed to think the Colonel was a complete gentlemen.

Two days later she ran into John Sheppard again. He and his team had come into the infirmary after a mission. He was filthy, dishevelled and had a several nasty scratches on his ribcage. She would have been quite content to continue cleaning bed pans, rather than speak to him, but Dr Beckett had called her over to help. He'd finished his scans and sent the Colonel to shower.

"When the Colonel comes back, could you clean those scratches, thanks love." Beckett had asked.

"Yes Doctor." She nodded, kind of nervous at the thought of having to be so close to the man.

Thankfully by the time Sheppard had returned to his bed, that noisy, whiny scientist, and the gorgeous warrior woman Teyla had arrived. Teyla had led Katie's induction session to the city, and she smiled sweetly at her.

The Colonel blushed as much as Katie did while she cleaned and dressed his wounds. At least "Mackay's" non-stop yabbering meant that they didn't have to talk to each other, although during a pause for breath, he did eye both the Colonel and Katie carefully.

"Hey is something going on here?" He blurted out.

"Rodney!" Teyla admonished and Sheppard growled "Mackay".

"Have we met? Dr Rodney Mackay, physicist not voodoo like Beckett." Rodney continued on unperturbed.

"Rodney this is Katie Thomas." Teyla told him while smiling broadly at Katie and rolling her eyes at Rodney. "Hello Katie." Teyla said sweetly.

"Hi, hello." Rodney cooed a little to smarmily for Sheppard's liking. "So you been here long?"

"Mackay, leave her alone!" He ordered.

"Oh a bit touchy there Kirk!" Rodney laughed.

"Just ignore him Katie! Have you meet John before?" Teyla asked.

Katie looked at John, and shook her head.

"Hi." She gave him a tight smile. "I'm all done. Dr Beckett said you have to stay overnight and rest." She turned and looked straight at Rodney. "Please keep the noise down Dr Mackay, or you will have to leave."

With a nod to Teyla, she picked up the basin she had been using and left the cubicle.

Rodney harrumphed as she walked away. "Well she's not very friendly!" He protested.

"I think she was very professional." Teyla disagreed.


	2. Chapter 2

It was just John's luck to end up with an infection from the scratches. He'd hoped to escape the confines of the infirmary and from the possibility of having to have a very uncomfortable conversation with Katie Thomas, but Carson threatened to put him in restraints if he didn't co-operate.

It was his third night in "prison" before his next encounter with Katie.

"Look I..." He started when she was taking his blood pressure.

"It's ok, forget it." She told him. She was still a little freaked, but she didn't get a bad vibe or anything from him, so she had decided to forget the, what should she call it? Incident?

"I don't know how I ended up in your room. I'm sorry. I don't normally sleep-walk or anything." He was flustered, rubbing a hand up the back of his neck. "I don't do stuff like that." He apologised.

"It's okay, really. Some of the other nurses told me that odd stuff happens here a lot." She undid the cuff and looped the stethoscope around her neck.

"No look, I'm really sorry I don't normally, ah, I don't sleep around or anything like that." John stammered. What the hell was he telling her that for? Not that he did, but why did he pick now of all times to get verbal diarrhoea?

"Sleep?" A familiar Scottish voice chirped. "You having trouble sleeping Colonel?" Carson asked as he pushed the curtain aside and appeared at the foot of the bed.

"Ah.. yeah, nuh." John blushed. How much had Carson heard?

"Ookay, no troubling sleeping, just forming sentences!" Carson smiled. "Never mind, Katie dear would you make sure the Colonel takes his meds before he goes to sleep." He gave John a cheesy grin. "He's a crafty beggar, make sure he swallows the pills, not palms them off!"

"Geez Doc it was one time!" John protested.

"One time too many. Now be a good lad and .." Carson didn't finish his sentence because Katie yelped and snatched her hand back from the monitor she had been checking. "You okay love. Let me see."

"It's okay, it just zapped me!" She said shaking her hand before surrounding it to Carson.

"No damage. You sure you're okay?" Carson gently turned her hand over in his.

"Yeah, just a shock I guess." She smiled coyly at her own pun.

"Yes well, we might as well just unplug the Colonel, he doesn't need it anymore. I'll get Zelenka's boys to check it out. Can't have it trying to electrocute people!" Carson said, unplugging John from the machine and wheeling it away.

"You okay?" John asked, his own eyes a little wide.

"Yeah, are you?" She looked at him closely. "Did it zap you too?" She thought his hair was standing a little more on end than usual.

"Nah!" It did but John wasn't going to say anything.

"I think you're lying to me." She told him.

"Just add it to my list of crimes." He shrugged. "Hey I wanted to say thanks for the other day, with Rodney." He changed the subject.

"What was I going to say? No we haven't been introduced but I did sleep with him one night last week?" She laughed.

"Yeah I guess not." John chuckled, his face turning red when he remembered that he had been naked at the time.

The talk was kind of awkward but it was better than trying to avoid each other in the confines of the infirmary.

000

A week later John woke up shivering in strange room. He went to get up off the cold floor and realised that he was only wearing his boxers and a sock on his right foot. Looking around him in a panic, he couldn't see his clothes anywhere.

"What the hell?" He asked no-one in particular. Had he been sleep walking again? The last thing he remembered was taking a shower then collapsing into bed. Checking his watch it was after 9 in the morning. He could hardly walk through the city in his underwear at this time of day, so he reached up for his radio for someone to bring him some clothes, but his earpiece was missing.

"Great, just great!" He grumbled.

Walking around the room he turned on a console so he could find out where he was. As he guessed he was in one of the unused labs and his only choice was to use the intercom to call someone for help. But who could he call that wouldn't ask what he was doing in an old lab in his underwear? Who wouldn't dob him into Carson for sleep-walking? Scratching a frustrated hand through his hair, he realised that there was really only one person he could call. Katie Thomas. Anyone else would probably have him sent for psych evaluation.

It took some fiddling but John was finally able to work out how to locate a person within the city by identifying their implanted tracker. It appeared Katie was in her quarters. Taking a deep breath John buzzed her intercom.

"Hello?" She answered after a few moments.

"Katie?" John wanted to make sure he was talking to the right person. He could tell from the monitor that she was alone, at least that was something.

"Yes?"

"It's John. John Sheppard."

"Is something wrong?"

"Well yeah, it's kind of well... one of those weird things again.." He started.

After explaining, John leant against the console to wait for Katie to bring him some clothes. He rubbed a hand through his hair again. What the hell was wrong with him? He'd never sleep walked before. Maybe it was the antibiotics he'd been taking? Maybe it was something in the food they'd been trading with the Athosians? Whatever it was, he'd have to ask Atlantis to not open his door unless he was fully conscious. He had no desire to wake up somewhere more public in his underwear.

It seemed to take forever before Katie arrived.

"Sorry I got lost. This place is like a maze." She told him handing over the clothes she'd collected from this quarters for him and to his delight, the boots he'd forgotten to ask for.

"Thanks." John told her but froze when he realised she was staring at him. "What? What's wrong?"

"What's up with your hair?" Her smirk, turned into slight giggle.

"Oh!" John reached up and ran a hand through his hair in alarm. His hair was standing on end.

"Does it always do that?" She asked.

"Yeah! Cowlicks." He grunted, kneeling on one knee to lace up a boot.

Katie didn't know what made her do it but she took a step closer to him. She had reached out and had her hand in his hair before she realised what she was doing.

"Sorry." She backed up a step. "I don't know why I did that."

"S'ok." He looked up at her with a confused look on his face. "I know how you feel, trust me!" John switched to do up the other boot, his scalp tingling where she had touched it. "I touched a crystal off-world once and ended up being everyone's worst nightmare for a week."

"Can I?" She asked, wriggling her fingers at his head.

"Sure." John shrugged he could hardly say no to the person who had saved him from a humiliating stroll through the city in his underwear.

She ran her hands through his thick hair, trying to re-direct the wayward strands to her satisfaction. John had to stamp down an impulse to reach out, wrap his arms around her and press his face to her stomach. He felt like an animal desperate to be petted and he almost whined in disappointment when she stepped away from him again.

"Not much of an improvement but at least you don't look like you've just rolled out of bed." She told him.

"Thanks. Not that anyone will notice. Mackay tells everyone who'll listen that I don't even own a comb." He said, buckling up his belt.

"Ah Dr Rodney Mackay, physicist not a voodoo doctor!" She smiled.

"That's him. I do, you know, own a comb." Why did he feel the need to tell her these things?

"I believe you." She frowned.

"It just grows like this. I need a haircut, it's not regulation. My last CO in Antarctica didn't really care so much about the regs you know. Bit more relaxed here too. Normally I just buzz it, but I've been a bit busy lately." John wanted to smack himself in the forehead. He was acting like Rodney, jibbering on like an idiot, but he couldn't stop himself.

There was an awkward silence for a moment before John suggested they should head back to civilisation.

As they walked through the hallways neither mentioned the conversation they'd just had in the lab, or his idiotic yammering. In fact they didn't speak until they stepped out of the transporter.

"Thanks." He said again.

"Don't mention it." Katie smiled and headed back to her quarters.

John was late for his morning meetings. So he headed for Woolsey's office unshowered, starving and more than a little freaked out. What the hell was wrong with him? He'd woken up twice in strange places and yabbered on like an idiot to a woman he hardly knew. Just thinking about her made his scalp tingle at the memory of her touch. And why did he seem to be drawn to her?


	3. Chapter 3

John headed for his quarters, he'd spent a long bruising session with Ronon in the gym and he stank! He just wanted a hot shower, and to lay down in the darkness for a while, to let his aching muscles relax and try to get his head sorted out.

He hadn't done anymore sleep walking lately. Well that he knew of! The first couple of nights he'd slept fully clothed, just in case he woke up somewhere more public than last time. He'd made sure his door was locked to stop himself making any further nearly-naked strolls around the city in his sleep.

John had even tried his best not to blush like an idiot whenever he saw Katie. That was the hardest part. Every time he saw her, he would remember how he had woken up naked in her bed. More difficult was trying to hide the paranoia that had been building inside of him, from his team. If anyone found out about his nocturnal, unconscious near-naked wanderings he would end up under psyche evaluation and taken off active duty.

In addition to the sleep-walking, he'd been having strange dreams of golden coloured whales, and of stars that smelt like flowers. He had dreamt of Katie Thomas, well the woman looked like her, similar face and hair, but her eyes glowed purple. She was smiling and he was holding her hand, they were looking down over the city fondly, while strange whale song soared around them and the city glowed in a hazy golden light.

John was used to having pretty vivid dreams, well nightmares really. Afghanistan, Koyla, Ford, Sumner all plagued his dreams and it wasn't unusual for him to wake in a tangle of sweaty sheets and adrenalin fuelled panic. It wasn't the fact that he was having these strange dreams instead of his regular nightmares that really disturbed him. It was the fact that at times he was sure he could hear that weird whale song when he was awake.

John yawned as he paused at his door, placing his hand on the internal controls. He hoped Atlantis understood that he wanted her to keep his door locked, to not let anyone in and definitely don't let him out until 6am, unless there was an emergency. Just to be sure he pulled out one of the control crystals from the panel.

000

John wiped the steam from his bathroom mirror and looked at his reflection. He ran a hand through his too-long disagreeable hair, trying to flatten it down. Maybe he should buzz it off, like he'd told Katie. He always used to wear it that short, until McMurdo when it didn't seem so important to be the perfect Air Force officer anymore. At least it would shut Rodney up.

Rodney! It pissed John off that Rodney seemed to imply that he was a prissy fly-boy who spent hours in front of the mirror perfecting his "look". John knew he did okay in the looks department but he wasn't that vain. At the most he ran a bit of gel through his hair in the morning to try and weigh it down a bit, but with little success.

He opened the cabinet door and pulled out his clippers. He reached over to plug them in but the adaptor plug was missing. He frowned. He was sure that there had been one there last time he looked. He had another adaptor somewhere in his room, but right now he was too tired to look for it. So he decided to leave his hair until the morning. He just wanted some sleep. Preferably sleep in his bed, not on the floor in some strange lab. Switching off his bathroom light, John headed for his bed.

000

When John did wake up he was in his own bed, however he instantly knew that something wasn't right however because someone was sitting next to him. He smelt something sweet and floral, like perfume.

"Katie?" He whispered into the gloom.

"Hi John."

"Is everything alright?" He leaned up on an elbow. How had she gotten into his room? Without the crystal there was no way she would have been able to open his door.

"Yeah, just thinking."

John thought she sounded kind of odd, distant. Maybe she was a sleep-walking, sleep-talker, if that sort of thing existed.

"What about?" John asked.

She shuffled next to him slightly and John felt the familiar tingle as she ran her hand through his hair. John had to bite his lip to stop a moan escaping him.

"You're not really going to cut your hair are you?"

"Yeah, in the morning." Whatever was going on here was so bizarre that curiosity convinced him to play along.

"Don't!" She told him. "I like your hair. I like your scruffy nerf-herder look."

"Did you just quote Princess Leia?" He gave a nervous laugh.

"Mmm!" She murmured, and then she kissed him.

A small fragment of John's brain told him this was wrong, but every other part of him shouted for it to shut the hell up! If he wasn't fully awake before, he was now! Every part of him tingled and his tongue seemed to move of its own accord, searching out hers. Finally his self-control returned and realised he had to stop this.

"John?" Katie asked before he could act. "What's happening?"

John opened his eyes and was shocked to find his room seemed to be lit up by millions of tiny golden fireflies. The waved his hand in the air and the light passed right through it.

"I don't know!" He panted, still a little breathless from the kiss.

"I don't remember coming here." Katie sounded lost, confused. John knew the feeling.

John reached over to pick up his earpiece to ask someone in engineering to check for odd readings in his quarters when the fireflies turned red and swirled around his hand. His hand tingled uncomfortably and he pulled it slowly back to his chest. The lights returned to their happy golden colour and buzzed around the bed, enveloping him and Katie. She looked at him in wide-eyed astonishment as the strange music the strange whale song from his dreams began to play softly.

The music was like a lullaby, soothing away concerns, cocooning them both. He felt Katie slide down onto the bed and snuggle into his chest. John's head felt light, like he was disconnected with reality. He closed his eyes and let the music lull him to sleep.


	4. Chapter 4

When John's alarm buzzed he begrudgingly unglued his eyelids to see it was 5:30am. Throwing off the covers he was half way to bathroom when he remembered that he had had a visitor last night. He was all alone in his quarters, frowning he walked over to the door and looked it over. It didn't look like it had been tampered with, the crystal was still missing.

He shook his head and walked back to the bathroom. He was so distracted by the strange dream from last night, that he dropped his razor, splattering himself with shaving cream and managing to slice his finger open when he'd made a grab for the blade. Cursing he stuck his still soapy finger in his mouth before he could stop himself. Spitting out shaving foam, he bent down to pick up his razor from the floor. As he stood back up he spotted the adaptor plug sticking out of the wall.

He distinctly remembered that plug was missing last night. Thinking it was weird, he opened his shaving cabinet in search of a sticky plaster for his finger, to get another surprise. His clippers were missing. What the..? John rubbed at his forehead as if it would clear his confusion, and delay the headache that was threatening. His finger was refusing to stop bleeding and reluctantly he knew he'd have to visit the infirmary, perhaps Carson would be willing to share a few Tylenol as well?

Katie was on duty when John arrived at the infirmary with his hand wrapped in a towel.

"What have you done this time?" She heard Carson's familiar brogue call out across the room.

"Just cut my finger." John tried not to blush, as Carson unwound the towel and tutted loud enough that everyone in hearing range could hear his disbelief.

"Right then. Katie dear, I'll need a suture kit please." He turned back to John. "Really Colonel you need to be more careful, what was it this time? Knife fighting with Ronan?" Carson continued.

"Dropped my razor and made a grab for it before I realised." John admitted. "Hey Doc, you couldn't swing me a couple of aspirin could you, gotta a headache coming on."

Carson raised his eyebrows at his friend.

"Nothing sinister, just over tired. I haven't slept well the last couple of nights. Too much going on you know." John explained.

"Are you being honest with me Colonel?" Beckett narrowed his eyes at gave John a closer look.

"Yeah yeah, maybe I'll get Lorne to cover for me this morning and try catch a nap."

000

Half an hour later John was back in his quarters, the proud owner of two stitches, and ready for a nap. Carson had practically forced a sleeping pill down his throat. Sitting on the edge of his bed, John unlaced his boots and kicked them off. His room looked exactly as he'd left it. Laying back on the bed he looked over at the poster on his wall.

"Keep an eye on everything for me Johnny." He slurred and drifted into sleep.

000

When John slowly woke it wasn't to the normal fuzzy hangover that sleeping pills gave him, but to a sensation of tranquillity and a pair of soft lips at his neck. Opening his eyes he saw the glow of the fireflies illuminating the room, dancing to that strange alien whale song.

John couldn't make his brain react to the strange happening in his room with anything more than mild recognition. He looked down at Katie and felt a rush of warmth. Everything seemed more intense through the haze of golden light that enveloped them. His hand slid into Katie's hair and he gently turned her face up to his and kissed her. John felt strangely disconnected with his body, unable to control its movements. He could feel the fabric of her shirt as his hand slid into it. He could feel the heat of her skin, the beating of her heart, but he couldn't make his hand stop. Not that he was convinced he wanted it to.

Enveloped in their golden cloud, Katie looked up at John, his handsome face illuminated by the golden light. Being in the cloud was like floating in warm water, calming, relaxing and all the while the music, the song, cajoled, soothed. She looked into John's eyes, the lids blinking lazily and his pupils the golden colour of the fireflies.

John's mind had given up trying to tell him something wasn't right with the situation. His thought processes were so dulled so that all he understood was desire and want. His hands travelled of their own accord over her Katie's body, tugging off the clothing that interfered with their path. His lips sucking at her skin, tongue licking, drowning in her scent. Even lost in his own activities he was aware of her of hands massaging his happy places.

Lips met, hands massaged, explored, tingling with electricity, and the fireflies turned pink, humming their song. The music soothed and soared at the same time, encouraging, turning attraction to desire, to need, and in a blanket of purple tinkling stars, to ecstasy.

John knew these feelings were not all his own. Not all Katie's either. Something else, someone else was with them. A little part of his brain recalled his bonding with Chaya, but this was different, this was more complete. Was this what it was like to ascend?

Looking down at Katie, her eyes were the same purple as the fireflies and John vaguely knew his were the same. His energy spent, John laid beside her and pulled her into his arms.

It was still daylight when John woke again, still in bed, still holding Katie. He could still feel a touch of the peculiar joyful lassitude he'd felt hours earlier when the strange fireflies had taken over his body.

She said his name, startling him from his daze.

"Katie?" He said, as he was saying the word for the first time.

"Let go John." She said quietly.

"Sorry." He mumbled and lifted his arm off of her.

She slid out of the bed and headed for the bathroom. After a few moments he heard the shower turn on and unable to ignore his bladder, John headed for the bathroom himself. He ducked into the toilet and closed the door. Enough of his senses had returned that he wondered what exactly to say to Katie. Last night was, well, he didn't have any words for it, only sensations, images.

Washing his hands in the sink he looked into the mirror. Almost absentmindedly he reached up and tried to brush his hair down. His minded was still a little foggy, like his head was full of fluff. He didn't even flinch when he distractedly noticed his eyes glowed an inhuman shade of gold.

He turned towards the shower, drew back the curtain and stepped into the cubicle. Katie looked up at him, hair darkened by the water and her eyes still flickering with the purple of the fireflies. John pushed her towards the wall of the shower and bent slightly to press his mouth hers, his hands moving of their own accord.


	5. Chapter 5

It was late in the afternoon when Rodney McKay burst into John's room. Wearily John raised his head from his pillow.

"You're in bed! The whole base has been looking for you and you're still in bed!" Rodney shrieked.

"Wha?" John blinked his fuzzy eyes at his watch. It was 4 in the afternoon.

"Do I have to get Lorne and the Marines to drag your lazy arse out of bed?" Rodney ranted.

John sat up, flipping the sheet back.

"Will you put some clothes on!" Rodney shrieked, turning his back to John and dramatically covering his eyes.

"Okay okay!" John grumped. "What's the problem?" The reached over and yanked his pants from the floor. He didn't remember getting undressed when he laid down this morning.

"Problem? Oh no problem that Lt Colonel Having A Sleep-in needs to worry about!"

"McKay!" John growled.

"Fine, fine. Just massive crazy energy readings, a missing Colonel who won't answer his radio, you know, same old same old!" Rodney jabbered.

"Energy readings?" John said alarmed. "Good or bad?"

"Don't know, we're checking now. You'd better get yourself up to see Woolsey right now though, he's on his second litter of kittens for the day!"

"Great!" John grabbed his earpiece and strode out the door with Rodney jogging after him. It was only as he headed for the transporter that he realised that he had been alone in his room when Rodney had burst in. Was that another dream? Maybe he was really losing his mind.

John couldn't decide if Woolsey was pleased or pissed to see him.

"Colonel thank you for joining us." He waved a hand towards the free chair in his office.

"Sorry, Carson made me take a sleeping pill this morning." John apologised. "Haven't been getting much shut-eye lately."

"Ah well, I understand." Woolsey nodded and continued. "There have been some strange readings in the city over the this morning. Drs Mackay and Zelenka and working on it now. Are you alright, you look a little odd." Woolsey was looking him up and down.

"Yeah, I haven't eaten since last night." That was the truth, John's stomach grumbled in agreement.

"Ok, well why don't you get something to eat and take something to Dr McKay before he eats Dr Zelenka." Woolsey almost smiled.

"Is everyone else okay?" John asked.

"Yes, although we need to find out what caused these energy spikes. Hopefully it is not another one of those energy creatures you encountered before."

000

The next few days went by in a haze of bickering scientists, fruitless searches of the city and the usual everyday craziness that happened on Atlantis. John was still having strange dreams, although nothing as intense as the day of the weird energy readings. He knew he should probably tell someone about what had been happening to him, but how could he do that without being locked up in the loony-bin? He'd been off-world and had another one of Carson's medicals and nothing was found, so the only reasonable answer could be that he was delusional.

After Ronan had nearly ripped his head off in a sparring match he made up his mind. This weird whatever-it-was was doing his head in. He decided he needed to find Katie. He needed to make sure that she was not some extra-terrestrial messing with his mind. It didn't take long to find her. She was at work in the infirmary.

"Hello Colonel." She said pleasantly as he walked into the infirmary.

"Hi. I was wondering if you had a moment to talk?" John asked.

"Not right now, maybe when I get off shift?" She suggested.

"Okay, what time do you finish?"

"At eight. Do you want me to meet you at your quarters?" She guessed that whatever was bothering him would be best discussed in private.

"Yeah that's be great." John smiled and headed back to his room.

While he waited, pacing back and forth, running his hands through his hair and rubbing at his forehead, John tried to come up with a way to open the conversation.

He discounted quite a few options, especially the "Hey Katie I think we might have had weird glowy sex a few nights ago but I'm not sure if I dreamt it or not." Or the "I've been having these weird dreams where you have glowing purple eyes and we had sex in my shower." Nope, both of those would probably end up with him getting a black eye, his boys bruised and on a harassment charge.

John spun around as his door slid open. It was Rodney.

"What?" John barked.

"Well hello to you too! Did you miss your afternoon nap?" Rodney snarked.

"Sorry, got a lot on my mind at the moment. What do you need?"

"You okay?" Rodney asked looking him over. "You look kind of ...odd."

"I'm fine Rodney, what do you want?" John tried to keep his tone friendly, normal.

"Just wanted to let you know I've got a track on those energy readings. I'm running a diagnostic now, it should be finished in an hour or so."

"Ok?" John prompted.

"I thought you might want to come down and have a look."

"Oh right. Give me and hour so, I've got something to finish up first." John told him. Possibly his career if he was really going nuts.

"Ok." Rodney nodded and headed for the door. "You should go see Carson, get something to help you sleep, you look like crap." Rodney said as the door slid shut.


	6. Chapter 6

Finally eight o'clock ticked closer and John started pacing again. He was getting a little sweaty when his balcony doors swung open to let in some fresh air.

His door slid open and Katie stepped into his room The door swished shut behind her and the control crystals glowed goldenly, unnoticed by the rooms occupants.

"John are you alright?" Katie asked, noticing how agitated he was.

"Yeah I'm fine." He lied, still feeling incredibly anxious.

"Why don't you sit down." She suggested. "You look tired." John looked fraught and ready to collapse.

"Sure." He did as he was told and sat on the end of the bed.

Katie moved to stand next to him. He looked up at her as she reached over to run her fingers through his messy hair.

"Silly nerf-herder, you're a mess." She smiled.

"What?" John eyes went wide as he looked up. Her eyes turned the familiar purple and her hands dropped to rest on his shoulders. "Katie?"

"She's here with us John." It was Katie's voice, but she hadn't spoken. Somehow her voice just appeared in his mind.

"Us?" He felt panic begin to well in his chest.

"Can't you feel me John?"

And suddenly he could feel they weren't alone. He felt a presence in his mind.

"Are you another consciousness like Phoebus and Thalan?" He asked.

"Not like Phoebus and Thalan. Don't you know me?" She smiled with Katie's smile. "Does this help?"

John heard his balcony doors close and the room began to glow with thousands of golden fireflies.

"Atlantis!" John said in barely a whisper. He could feel the city, feel her happiness that he recognised her. "Why are you doing this?"

"You are very important to me John. I want you to be happy. I don't want you be alone anymore. I chose Katie for you." The City sounded pleased with herself.

"You chose? What about what Katie wants?" John protested.

"Katie likes you very much John." Atlantis told him. "I have not controlled your interactions, only encouraged you towards intimacy. Children like yourself are often slow in these regards."

"Does Katie know that you are using her like this?" John ignored the 'children' comment.

"Of course John. She is with us and allowing me to communicate with you."

"How, how can you do this?" John frowned.

"The gene that sets you apart from the other children exists in Katie as well." Atlantis patiently explained. "It allows me ... access to you."

"What do you want from us?" John wasn't sure he really wanted the answer that question.

"Just your happiness. I have felt your loneliness John. I had begun to fear you would leave me to find a companion."

"So you picked a girl for me so I wouldn't leave home?" John was acutely aware of having a similar conversation with his father many years ago.

"I simply wish for all of my children to be happy. Did you not feel bond with Katie when you first met, have you not found comfort with her, have you bonded with her more closely than the other children?"

Maybe that explained all of his random jabbering and the dreams. It took him a long time to let down his guard and let someone get to know him intimately, perhaps he was comfortable with enough to do that with Katie?

"What are you?" How could a city be sentient? This was more than a gene making doors open and close.

"When the people that you call the Ancients built this city they called out to the heavens for guidance and I came to them, inhabited the cold place they had built and gave it life. I became your city. You could say that I am the heart of Atlantis."

"Did you talk to them as well?"

"No. They were too concerned with their own achievements to accept my presence. You are more open to me. More willing to learn and give. You have given me the gift of happiness with your presence. I wished only to share that joy with you, but when I sensed your growing discomfort and I knew I must communicate with you more directly."

"What happens if Katie and I aren't as compatible as you think?"

"Your future is for you to decide I have simply given you the opportunity. I must leave you John, your Rodney McKay is searching for me. He is a most intelligent and determined child."

"One last question. Why Katie?" John bit his tongue. He'd forgotten she'd hear the answer to his question as well.

"That is easy. Children with the gene have always been more likely to couple with their own. It is a survival mechanism inbuilt into your very cells. Other than the gene itself, the first time you saw Katie in the room with the Ancestral Ring, I detected an increase in blood pressure and a hormonal stirring within you."

"Great!"

"I must leave John. Happiness to you, child."

John caught Katie as her legs wobbled and her eyes returned to their normal colour.

"Are you okay?" He asked helping her to sit down.

"That was weird!" She breathed a few deep breathes.

They sat in silence for a time.

"I feel like I've been set up on a date by my Mom." John admitted.

They both laughed awkwardly, then sat silently on the bed for a few moments longer.

"Did she speak with you as well?" John wondered if Katie had her own conversation with Atlantis.

"Not really, I heard your conversation but I could feel that she is very fond of you. I think you're her favourite."

"Yeah I got that." John scratched behind his ear to try and hide his embarrassment. He'd been set up on blind dates before but this was something else.

"And apparently I'm fond of hormonal Star Wars fans with crazy hair." She gave him an embarrassed smile.

"So.." John wasn't sure what to say, or do.

The shower suddenly turned on in the bathroom.

"I think your Mom's trying to tell you something." Katie laughed.

"I guess she thinks I need a shower!" John shook his head, and lifted his shirt for a sniff. He was pretty sweaty and nasty after his time with Ronon.

"Puts a new spin on Mother Knows Best!" She grinned. "If you want to talk some more, I can wait."

"Yeah. Yeah good idea." John stood up, swiping his track pants from the bed on his way.

Katie leant back on his bed and watched as John disappeared into the bathroom. She smiled for a moment admiring the view, then got up and followed him.


	7. Chapter 7

John sat in his office waiting to be called into the room where General O'Neil and Woolsey were discussing his future with the IOA via video link. He was sweating, and the collar of his uniform felt like it was way too tight. He knew what was coming. They were going to fire him and send him back to Earth, where he'd probably be given at minimum a dishonourable discharge. Not that John wouldn't admit that he deserved it.

He'd withheld information, he'd lied to his superiors and he'd acted inappropriately with a member of the expedition. Shortly he'd been unemployed, disgraced (again), and possibly in jail. Even worse, he'd be forced to leave Atlantis and would be leaving Katie alone, if he didn't get her fired too!

Frustrated at himself he scrubbed a hand through his prickly hair. Katie hated it that short but O'Neil had insisted it would work in his favour if he at least looked the part when the IOA crucified him. Hence that fact he was also wearing his dress blues. They hadn't spoken to him yet, and he was hoping that wasn't a bad sign.

Finally Major Lorne appeared at his door.

"Sorry sir I was looking for Colonel Sheppard!" Lorne smirked. "Maybe you've seen him around, slouches a lot, kind of chilled, has this weird hair that sticks up like he got an electric shock!"

"Very funny!" John blushed, self-consciously rubbing the back of his neck. "Why are you so cheerful, got a promotion I don't know about?" John poked back at him.

"Got a good vibe when Woolsey asked to collect you." Lorne smiled.

"Yeah?" John quirked an eyebrow at Lorne.

"He even smiled!" Lorne beamed.

000

"Ah Colonel thanks for joining us!" General O'Neil told him, returning John's salute. "Take a seat Dr McKay was about to finish explaining his findings."

"Yes yes! As I was saying the energy reading spiked nearly two months ago, the night Sheppard and the nurse well, got together the first time." Rodney cleared his throat nervously. "Since that time there have been various anomalies that seemed centred around one or other of them. So Zelenka and I started scanning various systems around the city and we started to see a pattern of movement in the energy readings. So we decided to check the video footage in those areas. In some of the footage both Sheppard and Nurse Thomas can be seen moving through the hallways towards the point of where the anomaly occurred shortly after."

"Right?" O'Neil prompted, giving him the get on with it hand signal.

"Well the interesting thing is that they were both behaving strangely, well they looked to be sleep walking."

"How could you tell?" Woolsey asked.

"Well we traced one journey of Sheppard's from his quarters to an abandoned lab in an unused part of the city."

"So?" O'Neil prompted again.

"Before he left his quarters he had been in bed for some time, then just got up and walked out in his underwear and strolled through the city down to an area that is unused."

"That something you do often Sheppard?" O'Neil teased. John felt the tips of his ears begin to burn red.

"Then there was the night of the first massive energy spike. This time it was Katie Thomas sleep walking." Rodney added.

"Could we get to the punch line? I don't want to miss lunch."

"Right. The energy signatures were coming from the city itself, and at the times of the spikes the energy signatures merged with the signatures of John and Katie. In effect the city itself was in control of them. We also found evidence that a sub-routine was started by the city's main systems to examine the personnel records of everyone in the city, and their medical records etc etc."

"And?" O'Neil waved his hand at Rodney in frustration.

"It's just a theory but we believe that Atlantis herself was trying to find Colonel Sheppard a mate. That the intention seemed to be to breed a new batch of individuals with a strong ATA gene."

"The city was creating its own breeding programme?" Woolsey summarised.

"Yes!" Rodney announced, smiling as is he was proud of the discovery. "We found the routine and have removed it from the city's programming."

"Okey dokey. So let me get this right. Atlantis, the flying city, slash ancient ship decided to start its own mating programme to breed new Ancients? I know Sheppard's gene is strong but why the girl?" O'Neil tilted his head to one side, as if trying to understand a difficult puzzle.

"Well that part is interesting. Nurse Thomas has the ATA gene naturally, not a very strong representation, but she is one of the only women in the city with a natural presentation, and she is also, according to Dr Beckett, at the optional age for child bearing."

That made John blush again, this time on Katie's behalf.

"And you've disabled this thing so it can't decide to mate Sheppard to a puddle jumper or something?"

"Yes." Rodney replied.

"Well then, I think we can call this sorted. So it was a computer glitch. I'll send you our reports." He said to the camera and shut off the screen with the remote, cutting the feed to the IOA. "Sheppard get back to work. Come on Dick, let's get some lunch." O'Neil stood up and was already heading for the door.

"General I..." Woolsey started, looking at the now blank screen but gave up when it was obvious the O'Neil wasn't waiting. "Very well." Woolsey rolled his eyes but moved to follow Jack. "Colonel your back on active duty, effective immediately. Dr McKay." He said with a relieved smile as he passed the two men.

000

"Thanks Rodney." John grinned at his friend.

"You're welcome." Rodney nodded. "Actually I'll just be happy to not have to see any more video of you wandering around the city in your underwear again!" He said as they headed for the Mess Hall. "I hear O'Neil bought a supply of frozen cherries and there'll be pie in the Mess."

"Race you!" John said as he shoved Rodney into the wall and trotted out of the room, leaving the scientist muttering in his wake.

000

John was in the shower when Katie arrived. She had just heard the news that the IOA had agreed with O'Neil and Woolsey's findings and John was in the clear. She sat on his bed to wait.

"Hi!" He said startled by her appearance in his room. "You okay?"

She stood and slid into his arms.

"Rodney told me about the hearing."

"He did huh?" John raised an eyebrow.

"Actually he was complaining about Ronon eating his cherry pie, but he did mention that you were in the clear." She laughed.

"Yeah." John nodded. "He's convinced it was just a glitch in the city computers, and unless She does it again I think they'll be none the wiser."

"Good. You want to grab some dinner to celebrate?"

"Are you asking me out on date?" He laughed.

"Might be."

"I thought you preferred scruffy guys!" He smirked, leaning down to kiss her.

She ran a hand up through his hair spiky.

"Promise you'll let it grow out again. Makes you look ... serious!"

"Yeah, it's ruining my image." John laughed.


End file.
